[Rcpp-devel] Mac problem (possibly not Rcpp's fault)

Tue Apr 5 20:00:49 CEST 2011

On Apr 5, 2011, at 1:09 PM, Romain Francois wrote:

> Le 05/04/11 18:58, Jay Emerson a écrit :
>> I'm making a guess that the R-Forge setup is having the same problems
>> as we are, though -- more than just RcppModels show that same bus
>> error.  Executive summary: I now have a local success, with his
>> information given below, as well as information on one of the
>> failures; it does indeed appear to be a compiler version issue, as
>> Romain suspected.  I'll badger the students again to make sure they
>> are up to date.
>> 
>> Thanks!
>> 
>> The success setup:
>> 
>> R version 2.12.2 (2011-02-25)
>> Copyright (C) 2011 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> $ g++ --version
>> i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5664)
>> Copyright (C) 2007 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.  There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>> 
>> $ uname -a
>> Darwin Taylors-MacBook-Pro.local 10.6.0 Darwin Kernel Version 10.6.0:
>> Wed Nov 10 18:13:17 PST 2010; root:xnu-1504.9.26~3/RELEASE_I386 i386
>> 
>> -------------------------------------
>> My other student (who couldn't succeed) has an older version it
>> appears.  She seems to think she installed the newest version of
>> everything, up apparently not.
>> 
>> dhcp128036180037:R-2.12.2 Grace$ g++ --version
>> i686-apple-darwin9-g++-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5493)
>> Copyright (C) 2005 Free Software Foundation, Inc.
>> 
>> dhcp128036180037:Week10 Grace$ uname -a
>> Darwin dhcp128036046230.central.yale.edu 9.8.0 Darwin Kernel Version
>> 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386
>> i386
> 
> This is it I guess. IIRC R is only currently supported for versions greater than leopard (10.5).
> 

Nope - we do support 10.5 (Leopard) of course. The difference above is that the latter student has probably an ancient Xcode installed (2.x) whereas we recommend Xcode 3.x (and require it for compatibility with CRAN binaries). It is available from ADC free of charge (the latest version for Leopard is Xcode 3.1.4)

Cheers,
Simon

> (adding simon to the cc, he probably knows better than my vague memory)
> 
>> On Tue, Apr 5, 2011 at 12:14 PM, Dirk Eddelbuettel<edd at debian.org>  wrote:
>>> 
>>> Hi Jay,
>>> 
>>> Thanks for posting here!
>>> 
>>> On 5 April 2011 at 11:59, Jay Emerson wrote:
>>> | I've Rcpp-ified the new package bcp (Bayesian change point analysis)
>>> | and it seems to work on Linux and Windows.  We're having some Mac
>>> | problems (and I don't have a Mac).  I have one current and one past
>>> | student, both getting similar problems in different ways.  For one,
>>> | she started with (I think) Rcpp installing properly, but the RESULT 1
>>> | bus error when trying to build bcp.  I recommended she rebuild R from
>>> | scratch using updated everyting; after doing so, she got a similar bus
>>> | error RESULT 2, this time in the process of trying to install Rcpp.
>>> | The other student has the same bus error.
>>> |
>>> | I've exhausted my guesses and recommendations.  I note the same bus
>>> | error appears in some RcppModel logs, at
>>> |
>>> | https://r-forge.r-project.org/R/?group_id=155&log=build_mac&pkg=RcppModels&flavor=patched
>>> |
>>> | ?? Any advice ??
>>> 
>>> Hm, it so happens that Romain committed something today (r2950) which seems
>>> to be around the same or similar spot -- I have not been hit by anything like
>>> it.  OS X uses g++ 4.2.1 which is starting to pose challenges as we are being
>>> pushed at the same time to use g++ 4.5 and even 4.6 (now in Debian unstable
>>> and already used by Kurt on CRAN tests).
>>> 
>>> We sort-of have 0.9.3 pre-releases; we are being hang-up by a modules issue
>>> right now we are debugging. Rcpp 0.9.3 may help you -- can you and your
>>> students try the version from my site at
>>> 
>>>   http://dirk.eddelbuettel.com/code/rcpp/Rcpp_0.9.3.tar.gz
>>> 
>>> I just put a new tarball there that corresponds to r2956 which is very
>>> current.  Passes R CMD check here... but it not 'officially released' so it
>>> bites your cat and sets your car on fire none of that is our business :)
>>> 
>>> Romain may have more pertinent help for the OS X issues.
>>> 
>>> Dirk
>>> 
>>> | Jay
>>> |
>>> |
>>> | RESULT 1:
>>> | xiao-yangs-macbook:Week10 Grace$ R CMD INSTALL bcp
>>> | * installing to library '/Library/Frameworks/R.framework/Resources/library'
>>> | * installing *source* package 'bcp' ...
>>> | ** libs
>>> | make: *** No rule to make target `Cbcp.o', needed by `bcp.so'.  Stop.
>>> | *** arch - i386
>>> | g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
>>> | -I/Library/Frameworks/R.framework/Resources/include/i386
>>> | -I/usr/local/include
>>> | -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
>>> | -fPIC  -g -O2 -c Cbcp.cpp -o Cbcp.o
>>> | /Library/Frameworks/R.framework/Resources/library/Rcpp/include/Rcpp/internal/export.h:
>>> | In function 'void Rcpp::internal::export_range__dispatch(SEXPREC*,
>>> | InputIterator, Rcpp::traits::r_type_primitive_tag)':
>>> | /Library/Frameworks/R.framework/Resources/library/Rcpp/include/Rcpp/internal/export.h:56:
>>> | internal compiler error: Bus error
>>> |
>>> | Please submit a full bug report,
>>> | with preprocessed source if appropriate.
>>> | See<URL:http://developer.apple.com/bugreporter>  for instructions.
>>> | make: *** [Cbcp.o] Error 1
>>> | ERROR: compilation failed for package 'bcp'
>>> | * removing '/Library/Frameworks/R.framework/Resources/library/bcp'
>>> |
>>> |
>>> | RESULT 2:
>>> | I downloaded Xcode 3.1.3 from the web and restarted the computer and
>>> | compiled R again. But Rcpp still cannot be installed; the error
>>> | message is the same:
>>> |
>>> |>  install.packages("Rcpp")
>>> | --- Please select a CRAN mirror for use in this session ---
>>> | Loading Tcl/Tk interface ... done
>>> | trying URL 'http://cran.stat.ucla.edu/src/contrib/Rcpp_0.9.2.tar.gz'
>>> | Content type 'application/x-tar' length 1921635 bytes (1.8 Mb)
>>> |
>>> | opened URL
>>> | ==================================================
>>> | downloaded 1.8 Mb
>>> |
>>> | * installing *source* package 'Rcpp' ...
>>> | ** libs
>>> | g++ -I/Users/Grace/Study/Statistics/2011Spring/STAT662/Week10/R-2.12.2/include
>>> | -I../inst/include/ -I/usr/local/include    -fPIC  -g -O2 -c Date.cpp
>>> | -o Date.o
>>> | ../inst/include/Rcpp/internal/export.h: In function 'void
>>> | Rcpp::internal::export_range__dispatch(SEXPREC*, InputIterator,
>>> | Rcpp::traits::r_type_primitive_tag)':
>>> | ../inst/include/Rcpp/internal/export.h:56: internal compiler error: Bus error
>>> | Please submit a full bug report,
>>> | with preprocessed source if appropriate.
>>> | See<URL:http://developer.apple.com/bugreporter>  for instructions.
>>> | make: *** [Date.o] Error 1
>>> | ERROR: compilation failed for package 'Rcpp'
>>> | * removing '/Users/Grace/Study/Statistics/2011Spring/STAT662/Week10/R-2.12.2/library/Rcpp'
>>> |
>>> | The downloaded packages are in
>>> |        '/private/var/folders/rB/rByzYYffEzadShxSslfirU+++TI/-Tmp-/RtmpNVHfDM/downloaded_packages'
>>> |
>>> | Updating HTML index of packages in '.Library'
>>> | Warning message:
>>> | In install.packages("Rcpp") :
>>> |  installation of package 'Rcpp' had non-zero exit status
>>> |
>>> |
>>> |
>>> |
>>> | --
>>> | John W. Emerson (Jay)
>>> | Associate Professor of Statistics
>>> | Department of Statistics
>>> | Yale University
>>> | http://www.stat.yale.edu/~jay
>>> | _______________________________________________
>>> | Rcpp-devel mailing list
>>> | Rcpp-devel at lists.r-forge.r-project.org
>>> | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>> 
>>> --
>>> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
>>> 
>> 
>> 
>> 
> 
> 
> -- 
> Romain Francois
> Professional R Enthusiast
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